Contacts of the helix formed by residues 82 - 111 (chain F) in PDB entry 3BVI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 82 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TRP* 3.6 19.8 - - - -
80F PHE 3.5 2.2 - - - -
81F GLU* 1.3 80.7 - - - +
83F LEU* 1.3 66.0 + - - -
84F THR 3.3 2.7 - - - -
85F GLN* 3.3 4.7 + - - +
86F ILE* 3.1 24.3 + - - +
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Residues in contact with LEU 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TRP* 4.2 4.6 - - - -
31F CYS* 4.3 5.2 - - - -
36F LEU* 4.1 18.5 - - + +
39F ALA* 3.6 31.4 - - + -
82F GLY* 1.3 70.3 - - - -
84F THR* 1.3 62.9 + - - +
86F ILE* 3.4 7.9 + - + +
87F PHE* 3.2 40.8 + - + -
141F ILE* 4.1 21.5 - - + +
151F LEU* 3.7 35.7 - - + +
154F ALA* 4.0 23.8 - - + -
155F ASP* 4.8 6.5 - - - +
158F VAL* 5.7 1.3 - - + -
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Residues in contact with THR 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F GLY 3.3 0.8 - - - -
83F LEU* 1.3 77.1 - - - +
85F GLN* 1.3 58.2 + - - +
87F PHE* 3.2 3.9 + - - +
88F GLN* 2.9 56.9 + - + +
138F LEU* 4.3 10.4 - - + +
141F ILE* 3.3 25.9 + - + +
142F GLU* 4.9 8.9 - - + -
146F ASN* 6.1 0.9 - - - +
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Residues in contact with GLN 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F LYS 4.7 0.9 + - - +
80F PHE* 3.4 21.9 - - - +
81F GLU* 3.0 55.5 + - + +
82F GLY* 3.3 14.9 + - - +
84F THR* 1.3 79.2 - - - +
86F ILE* 1.3 58.0 + - - +
88F GLN* 3.7 16.4 - - + +
89F LYS* 2.9 53.3 + - + +
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Residues in contact with ILE 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F MET* 3.6 28.7 - - + +
30F TRP* 3.4 37.9 - - + -
31F CYS* 4.0 13.0 - - - -
43F LEU* 4.0 22.0 - - + -
80F PHE* 3.7 31.0 - - + -
82F GLY 3.1 15.9 + - - +
83F LEU* 3.6 9.0 - - - +
84F THR 3.3 0.2 - - - -
85F GLN* 1.3 77.4 - - - +
87F PHE* 1.3 66.9 - - + +
89F LYS* 3.4 6.1 + - - +
90F ALA* 2.8 27.3 + - + +
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Residues in contact with PHE 87 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F ALA* 4.1 7.2 - - + -
42F PHE* 3.9 34.3 - + - -
43F LEU* 4.2 19.5 - - + -
83F LEU* 3.2 43.5 + - + +
84F THR 4.1 2.2 - - - +
86F ILE* 1.3 78.1 - - + +
88F GLN* 1.3 60.0 + - - +
90F ALA* 3.8 3.2 - - + +
91F TYR* 2.9 32.1 + - - +
134F PHE* 3.9 25.1 - + - +
137F ILE* 3.6 27.1 - - + -
138F LEU* 3.9 15.3 - - + +
141F ILE* 3.5 22.4 - - + -
158F VAL* 4.5 9.6 - - + -
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Residues in contact with GLN 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F THR* 2.9 31.3 + - - +
85F GLN* 3.7 23.6 - - + +
87F PHE* 1.3 76.7 - - - +
89F LYS* 1.3 61.8 + - + +
91F TYR* 3.7 1.7 - - - +
92F GLU* 3.0 38.2 + - - +
138F LEU* 3.7 26.4 - - + +
142F GLU* 4.4 9.7 - - - +
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Residues in contact with LYS 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 6.1 0.2 - - - -
27F MET* 3.8 11.9 - - + -
77F GLU* 3.3 38.6 + - - +
79F LYS 5.7 0.2 - - - -
80F PHE* 4.3 14.1 - - + -
85F GLN* 2.9 47.6 + - + +
86F ILE* 3.6 3.8 - - - +
88F GLN* 1.3 76.8 - - + +
90F ALA* 1.3 57.2 + - - +
92F GLU* 3.3 13.7 + - - +
93F HIS* 2.9 29.0 + - - +
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Residues in contact with ALA 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F TYR* 3.3 23.0 + - + -
27F MET* 3.9 10.0 - - - +
43F LEU* 5.1 2.0 - - + -
86F ILE 2.8 21.2 + - - +
87F PHE* 3.8 7.0 - - + +
89F LYS* 1.3 72.0 - - - +
91F TYR* 1.3 57.4 + - - +
93F HIS* 3.1 7.5 + - - +
94F GLU* 2.9 27.9 + - - +
134F PHE* 3.6 28.7 - - + -
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Residues in contact with TYR 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F PHE 2.9 19.0 + - - +
88F GLN 3.7 3.6 - - - +
90F ALA* 1.3 73.4 - - - +
92F GLU* 1.3 66.1 + - + +
94F GLU* 3.3 2.7 + - + +
95F GLN* 3.0 49.3 + - + +
131F GLU* 3.6 28.9 + - + +
134F PHE* 4.2 14.3 - - + +
135F LYS* 3.6 48.3 - - + +
138F LEU* 4.0 22.4 - - + -
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Residues in contact with GLU 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F GLN* 3.0 28.8 + - - +
89F LYS* 3.6 11.9 - - - +
91F TYR* 1.3 77.2 - - + +
93F HIS* 1.3 62.6 + - - +
95F GLN* 3.5 19.5 + - - +
96F HIS* 3.2 20.8 + - - +
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Residues in contact with HIS 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F LYS 5.3 0.7 - - - -
19F ASN* 4.8 10.5 - - - -
20F SER* 2.6 37.1 + - - -
23F LEU* 3.9 22.5 - - + +
24F TYR* 3.5 27.8 - + - -
89F LYS 2.9 14.3 + - - +
90F ALA* 3.1 12.5 + - - +
92F GLU* 1.3 77.7 - - - +
94F GLU* 1.3 58.7 + - - +
96F HIS* 3.1 17.1 + + - +
97F ILE* 3.0 42.3 + - + +
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Residues in contact with GLU 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F TYR* 2.5 31.4 + - - +
46F HIS* 2.9 22.5 + - - -
50F GLU* 3.7 1.8 - - - +
90F ALA 2.9 13.6 + - - +
91F TYR* 3.8 6.1 - - + +
93F HIS* 1.3 74.0 - - - +
95F GLN* 1.3 59.9 + - - +
97F ILE* 3.2 4.1 + - - +
98F SER* 2.9 28.1 + - - -
127F GLN* 2.9 24.5 + - - +
130F GLU* 4.0 4.6 - - - +
131F GLU* 4.2 16.6 - - + -
134F PHE* 3.9 20.4 - - + -
1007F FE 2.4 26.9 - - - -
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Residues in contact with GLN 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F TYR* 3.0 60.0 + - + +
92F GLU* 3.5 21.7 - - - +
94F GLU* 1.3 76.3 - - - +
96F HIS* 1.3 56.5 + - - +
98F SER* 3.4 2.9 + - - -
99F GLU* 3.0 29.2 + - - +
131F GLU* 3.5 24.8 - - - +
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Residues in contact with HIS 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F LYS* 3.0 37.6 + - + -
92F GLU 3.2 9.4 + - - +
93F HIS* 3.1 20.8 + + - +
95F GLN* 1.3 75.5 - - - +
97F ILE* 1.3 72.9 + - + +
99F GLU* 3.4 17.8 + - + +
100F SER* 3.0 23.4 + - - -
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Residues in contact with ILE 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F GLN* 4.1 9.6 - - - +
16F LYS* 4.4 25.6 - - + +
17F GLU* 3.8 20.6 - - - +
20F SER* 3.6 20.0 - - - +
50F GLU* 5.2 2.0 - - - +
93F HIS* 3.0 39.5 + - + +
94F GLU* 3.2 11.8 + - - +
96F HIS* 1.3 81.0 - - + +
98F SER* 1.3 65.3 + - - +
100F SER* 2.7 20.4 + - - -
101F ILE* 3.0 13.4 + - + +
127F GLN* 3.7 22.7 - - - +
1006F FE 3.9 0.9 - - - -
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Residues in contact with SER 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F GLU 2.9 10.4 + - - -
95F GLN 3.6 5.4 - - - -
97F ILE* 1.3 76.0 - - - +
99F GLU* 1.3 62.6 + - - +
101F ILE* 3.3 5.5 + - - +
102F ASN* 3.1 31.4 + - - +
127F GLN* 2.9 36.3 + - - +
128F HIS 5.0 0.3 + - - -
131F GLU* 2.5 31.4 + - - +
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Residues in contact with GLU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F GLN 3.0 18.1 + - - +
96F HIS* 3.5 18.3 - - + +
97F ILE 3.2 0.2 - - - -
98F SER* 1.3 74.6 - - - +
100F SER* 1.3 64.4 + - - +
102F ASN* 3.4 11.9 + - + +
103F ASN* 3.1 21.5 + - + +
----------------------------------------------------------
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Residues in contact with SER 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F GLN* 3.3 26.1 + - - -
16F LYS* 3.8 23.7 - - - +
96F HIS* 3.0 14.9 + - - -
97F ILE* 2.7 23.2 + - - -
99F GLU* 1.3 76.7 - - - +
101F ILE* 1.3 61.4 + - - +
103F ASN* 3.3 10.1 + - - +
104F ILE* 3.2 24.4 + - - +
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Residues in contact with ILE 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F GLN* 3.7 7.0 - - - +
97F ILE* 3.0 13.2 + - + +
98F SER 3.5 6.7 - - - +
100F SER* 1.3 80.8 + - - +
102F ASN* 1.3 65.7 + - - +
104F ILE* 3.0 11.3 + - + +
105F VAL* 3.0 25.3 + - + +
120F LEU* 5.4 3.6 - - + +
123F TYR* 3.7 46.2 - - + +
124F VAL* 3.8 31.6 - - + -
127F GLN* 3.4 40.6 - - + -
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Residues in contact with ASN 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F SER* 3.1 20.6 + - - +
99F GLU* 3.5 12.3 - - + +
101F ILE* 1.3 79.8 - - - +
103F ASN* 1.3 56.9 + - - +
105F VAL* 3.9 6.9 - - - +
106F ASP* 2.8 31.6 + - - +
124F VAL* 5.0 11.3 - - - +
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Residues in contact with ASN 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F LEU* 3.8 24.0 - - - +
99F GLU 3.1 14.1 + - - +
100F SER* 3.5 13.1 - - - +
101F ILE 3.2 0.2 - - - -
102F ASN* 1.3 73.7 - - - +
104F ILE* 1.3 58.9 + - - +
106F ASP* 3.8 9.2 + - - +
107F HIS* 3.0 29.8 + - - +
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Residues in contact with ILE 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ILE* 4.3 11.7 - - + +
9F LEU* 3.9 37.0 - - + +
10F LEU* 4.2 17.9 - - + -
13F GLN* 3.5 44.4 - - + +
100F SER 3.2 12.0 + - - +
101F ILE* 3.0 9.9 + - + +
103F ASN* 1.3 72.4 - - - +
105F VAL* 1.3 61.1 + - - +
107F HIS* 3.2 6.1 + - - +
108F ALA* 2.9 27.4 + - - +
116F THR* 4.9 0.9 - - + -
120F LEU* 3.6 25.8 - - + -
123F TYR* 5.6 0.7 - - + -
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Residues in contact with VAL 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F ILE* 3.0 20.2 + - + +
102F ASN* 4.0 7.2 - - - +
104F ILE* 1.3 74.8 - - - +
106F ASP* 1.3 63.4 + - - +
108F ALA* 3.1 8.6 + - - +
109F ILE* 3.1 25.0 + - + +
117F PHE* 3.4 33.2 - - + -
120F LEU* 3.7 25.1 - - + -
121F GLN* 4.4 5.2 - - - +
124F VAL* 3.9 26.9 - - + -
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Residues in contact with ASP 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F ASN 2.8 19.6 + - - +
103F ASN* 3.8 11.2 + - - +
105F VAL* 1.3 78.3 - - - +
107F HIS* 1.3 61.7 + - - +
109F ILE* 3.3 15.7 + - - +
110F LYS* 2.8 59.7 + - - +
----------------------------------------------------------
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Residues in contact with HIS 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ASP* 3.1 42.0 + - + +
6F ILE* 3.6 20.4 - - + -
9F LEU* 3.9 18.7 - - + +
103F ASN* 3.0 20.1 + - - +
104F ILE 3.2 4.2 + - - +
106F ASP* 1.3 75.7 + - - +
108F ALA* 1.3 63.9 + - - +
110F LYS* 3.9 12.7 - - + +
111F SER* 2.8 40.8 + - - -
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Residues in contact with ALA 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ILE* 4.0 11.6 - - + +
104F ILE 2.9 13.2 + - - +
105F VAL* 3.1 11.4 + - - +
107F HIS* 1.3 77.8 - - - +
109F ILE* 1.3 56.2 + - - +
111F SER* 3.5 5.3 + - - -
112F LYS 3.0 7.8 + - - -
113F ASP* 2.7 49.2 + - + +
116F THR* 4.6 6.3 - - + -
117F PHE* 4.0 19.7 - - + +
120F LEU* 5.3 0.4 - - + -
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Residues in contact with ILE 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F VAL* 3.1 17.0 + - + +
106F ASP* 3.6 14.4 - - - +
108F ALA* 1.3 75.9 - - - +
110F LYS* 1.3 66.9 + - + +
112F LYS* 2.9 17.7 + - - +
114F HIS* 4.5 20.8 + - + +
117F PHE* 3.6 34.1 - - + -
----------------------------------------------------------
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Residues in contact with LYS 110 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F ASP* 2.8 47.3 + - - +
107F HIS* 3.9 13.2 - - + +
109F ILE* 1.3 79.3 - - + +
111F SER* 1.3 60.4 + - - +
112F LYS* 3.5 7.8 + - - +
----------------------------------------------------------
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Residues in contact with SER 111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F SER* 4.8 9.1 + - - -
6F ILE* 4.2 4.3 - - - +
107F HIS* 2.8 38.0 + - - -
108F ALA* 3.5 7.6 + - - -
110F LYS* 1.3 74.4 - - - +
112F LYS* 1.3 70.0 + - - +
113F ASP* 3.3 11.9 + - - +
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il